geoseeq 0.6.14.dev6__py3-none-any.whl → 0.6.14.dev7__py3-none-any.whl

geoseeq/cli/main.py

@@ -55,7 +55,7 @@ def version():
     Use of this tool implies acceptance of the GeoSeeq End User License Agreement.
     Run `geoseeq eula show` to view the EULA.
     """
-    click.echo('0.6.14dev6')  # remember to update pyproject.toml
+    click.echo('0.6.14dev7')  # remember to update pyproject.toml
 
 
 @main.group('advanced')

geoseeq/cli/upload/upload_advanced.py

@@ -6,7 +6,7 @@ from .upload_reads import (
     _make_in_process_logger,
     _get_regex,
     _group_files,
-    flatten_list_of_fastqs,
+    flatten_list_of_fastxs,
 )
 
 from multiprocessing import Pool, current_process
@@ -84,7 +84,7 @@ def cli_find_urls_for_reads(state, cores, overwrite, yes, regex, private, module
     """
     knex = state.get_knex()
     proj = handle_project_id(knex, project_id, yes, private)
-    filepaths = {basename(line): line for line in flatten_list_of_fastqs(fastq_files)}
+    filepaths = {basename(line): line for line in flatten_list_of_fastxs(fastq_files)}
     click.echo(f'Found {len(filepaths)} files to upload.', err=True)
     regex = _get_regex(knex, filepaths, module_name, proj, regex)
     groups = _group_files(knex, filepaths, module_name, regex, yes)

geoseeq/cli/upload/upload_reads.py

@@ -118,7 +118,7 @@ def _is_fastq(path, fq_exts=['.fastq', '.fq'], compression_exts=['.gz', '.bz2',
     return False
 
 
-def _is_fasta(path, fa_exts=['.fasta', '.fa'], compression_exts=['.gz', '.bz2', '']):
+def _is_fasta(path, fa_exts=['.fasta', '.fa', '.fna', '.faa'], compression_exts=['.gz', '.bz2', '']):
     for fa_ext in fa_exts:
         for compression_ext in compression_exts:
             if path.endswith(fa_ext + compression_ext):
@@ -289,9 +289,9 @@ def cli_upload_reads_wizard(state, cores, overwrite, yes, regex, private, link_t
     [FILES...] can be paths to BAM files or a file containing a list of paths, or a mix of both.
     Example: "path/to/bam/files
     """
-    knex = state.get_knex()
-    proj = handle_project_id(knex, project_id, yes, private)
-    filepaths = {basename(line): line for line in flatten_list_of_bams(files)}
-    click.echo(f'Found {len(filepaths)} files to upload.', err=True)
-    groups = _group_files(knex, filepaths, 'bam::bam', regex, yes)
-    _do_upload(groups, 'bam::bam', link_type, proj, filepaths, overwrite, no_new_versions, cores, state)
+    # knex = state.get_knex()
+    # proj = handle_project_id(knex, project_id, yes, private)
+    # filepaths = {basename(line): line for line in flatten_list_of_bams(files)}
+    # click.echo(f'Found {len(filepaths)} files to upload.', err=True)
+    # groups = _group_files(knex, filepaths, 'bam::bam', regex, yes)
+    # _do_upload(groups, 'bam::bam', link_type, proj, filepaths, overwrite, no_new_versions, cores, state)

geoseeq/constants.py

@@ -2,7 +2,13 @@ from os import environ
 from os.path import join
 
 FIVE_MB = 5 * (1024 ** 2)
-FASTQ_MODULE_NAMES = ['short_read::paired_end', 'short_read::single_end', 'long_read::nanopore', 'raw::raw_reads']
+FASTQ_MODULE_NAMES = [
+    'short_read::paired_end',
+    'short_read::single_end',
+    'long_read::nanopore',
+    'raw::raw_reads',
+    'genome::fasta',
+]
 DEFAULT_ENDPOINT = "https://backend.geoseeq.com"
 
 CONFIG_FOLDER = environ.get("XDG_CONFIG_HOME", join(environ["HOME"], ".config"))

{geoseeq-0.6.14.dev6.dist-info → geoseeq-0.6.14.dev7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: geoseeq
-Version: 0.6.14.dev6
+Version: 0.6.14.dev7
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>

{geoseeq-0.6.14.dev6.dist-info → geoseeq-0.6.14.dev7.dist-info}/RECORD

@@ -2,7 +2,7 @@ geoseeq/__init__.py,sha256=YqYqeHbqjgWI5OBIxkPXNvLISOjVWaNwVFy6AGJ7uwc,982
 geoseeq/app.py,sha256=Y6d1UzxFLfE3RNccATbFCVi6kH3eFmzwoUbeR2Ry09A,2387
 geoseeq/blob_constructors.py,sha256=AkWpDQY0EdGMxF1p6eRspyHKubcUdiW4it-_Q7S2QWk,188
 geoseeq/bulk_creators.py,sha256=pdn-Dv7yv5SFv-PfDuQbuOnw2W4-BfIfRJVRAhM8U6s,2115
-geoseeq/constants.py,sha256=z_ninEd7WsS5DaLntdR-sqAFib6Ie22jlhPKzLvLerw,449
+geoseeq/constants.py,sha256=g9YEczT2ssteTrdgFrRimXo5I0C8-MqftoG-hE3KAkg,489
 geoseeq/file_system_cache.py,sha256=HzVZWtwLD2fjWWSo_UfWmGeBltm9He4lP_OqzKwNGWg,4138
 geoseeq/knex.py,sha256=zcjafsmUn9SC3LlRnvvaXpr-pHYZ0IXk7LpzuUoE3MI,8312
 geoseeq/organization.py,sha256=bJkYL8_D-k6IYAaii2ZbxjwYnXy6lvu6iLXscxKlA3w,2542
@@ -24,7 +24,7 @@ geoseeq/cli/download.py,sha256=cOLIVzAfxpOJnSd4WKWR-HCkOrKjPMbgYaNXDSd9i90,21305
 geoseeq/cli/fastq_utils.py,sha256=-bmeQLaiMBm57zWOF0R5OlWTU0_3sh1JBC1RYw2BOFM,3083
 geoseeq/cli/find_grn.py,sha256=oMDxkzGQBQb2_cCuvmwoeHOsFHqyO9RLeJzrB6bAe5M,439
 geoseeq/cli/get_eula.py,sha256=79mbUwyiF7O1r0g6UTxG9kJGQEqKuH805E6eLkPC6Y4,997
-geoseeq/cli/main.py,sha256=ufRoSCJh1D5jas9rZO6ypKRHTRh0jL2ET7fXAV5oD2E,3987
+geoseeq/cli/main.py,sha256=guwmM9RE-vVZcu7_rMyOLiet-Ua1Jw_VP0mk62cT4eQ,3987
 geoseeq/cli/manage.py,sha256=wGXAcVaXqE5JQEU8Jh6OlHr02nB396bpS_SFcOZdrEo,5929
 geoseeq/cli/progress_bar.py,sha256=p1Xl01nkYxSBZCB30ue2verIIi22W93m3ZAMAxipD0g,738
 geoseeq/cli/project.py,sha256=V5SdXm2Hwo2lxrkpwRDedw-mAE4XnM2uwT-Gj1D90VQ,3030
@@ -42,8 +42,8 @@ geoseeq/cli/shared_params/obj_getters.py,sha256=ZSkt6LnDkVFlNVYKgLrjzg60-6BthZMr
 geoseeq/cli/shared_params/opts_and_args.py,sha256=_DcJ-TqgrbBaeDd-kuHEx2gLZPQN6EHZYWh8Ag-d8Vg,2091
 geoseeq/cli/upload/__init__.py,sha256=3C9_S9t7chmYU-2ot89NV03x-EtmsjibulErKaU9w1k,627
 geoseeq/cli/upload/upload.py,sha256=JZkhe1q3KOp7-tKyzwi860TQhZoNDnZs4yB2PJhOjl0,10081
-geoseeq/cli/upload/upload_advanced.py,sha256=Jq5eGe-wOdrzxGWVwaFPg0BAJcW0YSx_eHEmYjJeKuA,3434
-geoseeq/cli/upload/upload_reads.py,sha256=Q5gihBmQM9jQx0QSj5qPH8sc8CkVNE1_DD5JradXBdg,10990
+geoseeq/cli/upload/upload_advanced.py,sha256=tXP7SWaLbLay5FVtqOoj-oToBM1ha2NWzywMnE0Foeo,3434
+geoseeq/cli/upload/upload_reads.py,sha256=IlO-9b8dHbA-fx8FK_R0BwyoRgtqQUoowgXJcyx_O3k,11018
 geoseeq/contrib/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 geoseeq/contrib/ncbi/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 geoseeq/contrib/ncbi/api.py,sha256=WQeLoGA_-Zha-QeSO8_i7HpvXyD8UkV0qc5okm11KiA,1056
@@ -87,9 +87,9 @@ geoseeq/vc/vc_stub.py,sha256=IQr8dI0zsWKVAeY_5ybDD6n49_3othcgfHS3P0O9tuY,3110
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/test_api_client.py,sha256=TS5njc5pcPP_Ycy-ljcfPVT1hQRBsFVdQ0lCqBmoesU,12810
 tests/test_plotting.py,sha256=TcTu-2ARr8sxZJ7wPQxmbs3-gHw7uRvsgrhhhg0qKik,784
-geoseeq-0.6.14.dev6.dist-info/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
-geoseeq-0.6.14.dev6.dist-info/METADATA,sha256=Yg0PM7m43T1S2-aC-vXwJsQ4SDh1JqkUqAbL2qePFBk,4937
-geoseeq-0.6.14.dev6.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-geoseeq-0.6.14.dev6.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
-geoseeq-0.6.14.dev6.dist-info/top_level.txt,sha256=zZk7mmeaqAYqFJG8nq2DTgSQPbflRjJwkDIhNURPDEU,14
-geoseeq-0.6.14.dev6.dist-info/RECORD,,
+geoseeq-0.6.14.dev7.dist-info/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
+geoseeq-0.6.14.dev7.dist-info/METADATA,sha256=q9ZgGURnAxFyUKqLaF6J5db1e9rrrqEcQbGhJ8MmFUc,4937
+geoseeq-0.6.14.dev7.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+geoseeq-0.6.14.dev7.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
+geoseeq-0.6.14.dev7.dist-info/top_level.txt,sha256=zZk7mmeaqAYqFJG8nq2DTgSQPbflRjJwkDIhNURPDEU,14
+geoseeq-0.6.14.dev7.dist-info/RECORD,,